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iDigBio's Train the Trainers Georeferencing Update

The First iDigBio Train-the-Trainers Georeferencing Workshop is well into Day 4 now! Day one, participants and instructors met iDigBio PI Pam Soltis, Project Manager David Jennings, Biodiversity Informatics Manager Joanna McCaffrey, Cathy Bester, iDigBio Program Assistant and Kevin Love, the iDigBio IT magician who keeps us all in touch with one another and connected to the internet. Shari Ellis, iDigBio Project Evaluator, shared results of the iDigBio Pre-Workshop Survey for this workshop with all the participants.

Public Participation in Digitization of Biodiversity Specimens Workshop Report

iDigBio’s Public Participation in Digitization of Biodiversity Specimens Workshop was held on September 28-29 in Gainesville, FL.

Topics included the role of citizen science, ways to engage the public in digitization, methods to build public participant virtual communities, and an overview of biodiversity informatics software to facilitate public participation. Visit the workshop wiki page for links to the final agenda, the GoogleDoc, and the presentations.

iDigBio Editorial Policy for Original Content and Previously-Published Content

The purpose of the of iDigBio website and e-newsletter is to facilitate the dissemination of information and updates regarding the implementation of NSF grant #EF 1115210, and to inform the broader community about progress, opportunities and obstacles relevant to resource digitization related to natural history museums.

The iDigBio website and e-newsletter serves a broad readership including natural history museum curators, collections managers, technical specialists, volunteers, citizen scientists and the general public.

Standards Documentation: 
https://www.idigbio.org/sites/default/files/iDigBio%20Editorial%20Policy%20v0.pdf

iDigBio Image File Format Requirements and Recommendations

iDigBio’s mission requires that it be able to aggregate and distribute digital images of biological specimens, records, and other objects associated with specimens (e.g., labels and notes) generated by TCNs and other bio- and paleo-collections hosting institutions. Linked below is a document providing current iDigBio policy as well as recommendations for acquiring, processing, archiving, and distributing still, two-dimensional digital images. We recognize the importance of other image types, including three-dimensional images, and will expand this current policy through time as demand dictates.

Current version: https://www.idigbio.org/content/idigbio-image-file-format-requirements-and-recommendations-1

Version history: https://www.idigbio.org/biblio?f%5bkeyword%5d=443

Biodiversity Informatician, School of Life Sciences, Arizona State University (position announcement)

The School of Life Sciences at Arizona State University invites applications for a Biodiversity Informatician. This is an academic, non-tenure track faculty research associate appointment.

Arizona State University is a dynamic, progressive university dedicated to interdisciplinary collaborations, to rethinking university education, and to integrating excellence in both research and teaching. The School of Life Sciences (SOLS) at Arizona State University's Tempe campus is committed to strengthening its impact in the fields of biodiversity informatics research and virtual collections management. SOLS maintains organismal collections totalling more than 1.5 million preserved specimens, and has played an instrumental role in creating the Southwest Environmental Information Network (SEINet) which serves more than 2 million records and 100,000 images on-line.

The successful candidate will work in close collaboration with SOLS curators, collection managers, affiliated researchers and students to advise, develop, and implement database-driven web applications aimed at the electronic dissemination of biological specimen and observation records. Focal areas include the future development of SEINet and its underlying software platform Symbiota, amalgamation and synthesis of all SOLS virtual collections into a unified web portal, participation in novel biodiversity informatics research projects, and integration with other initiatives and services in this dynamic field (e.g. CAP-LTER, Complexity of Life, Global Names, GBIF, iDigBio). The selected candidate will assume co-leadership in developing successful externally funded informatics projects and will serve as liaison between ASU collections researchers and students, network administrators and other ASU information technology support staff. Additional responsibilities may include participation in the creation and implementation of a new teaching curriculum in the field of biodiversity informatics.

Candidates must have an advanced degree (M.Sc. or higher) in Biology or Computer Science, minimally three years of experience in biodiversity informatics research and software development, and a strong familiarity with biocollections data management (e.g. DarwinCore) and contemporary nomenclatural and taxonomic practices and standards (e.g. TDWG). Desired qualifications include participation in recent federally funded research projects in this field (NSF-ADBC program, iDigBio, GBIF, etc.), extensive experience with programming languages and database-driven web application development, and specifically, skills in database design and management such as AJAX, CMS (e.g. Drupal), HTML 5, CSS, SQL, XML, network and server administration and scripting languages (Java, JavaScript, Perl, PHP, Python, Ruby), familiarity with Web 2.0 programming technologies, high adaptability to meet new challenges, and evidence of strong verbal and written communication skills, including grantspersonship.

Salary will be negotiable, depending on qualifications. To apply, send a cover letter, curriculum vitae, and up to three other items of choice that represent the ability to work as biodiversity informatician to Anna Fields, attn: Biodiversity Informatician Search Committee, School of Life Sciences, PO Box 874501, Tempe, AZ 85287-4501, with electronic applications sent as PDF files to solsfacultysearch3@asu.edu preferred (mailto:solsfacultysearch3@asu.edu). The initial closing date for receipt of complete applications is October 14, 2012. For additional information, please feel free to contact Nico Franz (nico.franz@asu.edu) or Les Landrum (les.landrum@asu.edu). A background check is required for employment at Arizona State University, an equal opportunity/affirmative action employer committed to excellence through diversity. We especially encourage women and minorities to apply (see https://www.asu.edu/titleIX/). For additional information on the School of Life Sciences, please visit http://sols.asu.edu.

This announcement is also available as a PDF at http://sols.asu.edu/employment/pdfs/f12_bio_info_research_associate.pdf

Submitted by Nico Franz. http://franz.lab.asu.edu/

Herbarium Digitization Training Workshop

Thirty participants gathered at Valdosta State University September 16–18, 2012 for iDigBio’s first herbarium digitization workshop. About half of the diverse group represented institutions at the earliest stages of launching digitization programs. More experienced attendees sought strategies for refining their institution’s workflows, processes, and protocols. iDigBio extends special recognition and appreciation to Valdosta State for hosting the workshop, providing extensive on-site support, and for making technology available that ensured the workshop's success.

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Mobilizing New England Vascular Plant Data TCN Kick-off Meeting

After a flurry of summer planning activities and software and workflow development, the New England Vascular Plant TCN (NEVP) officially kicked off with a meeting at Yale Peabody Museum of Natural History on September 6, 2012. NEVP plans to digitize collections from 15 herbaria across New England, with a focus on creating a dataset that can be used to study the impact of climate change and land-use history across this region. 

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Workshop on Digitization of Small Herbarium Collections

In an effort to consolidate resources and facilitate digitization efforts for small collections in Michigan and across the Great Lakes, we are planning a workshop on Saturday, October 20th, from 9-4 at Central Michigan University. This workshop is sponsored by iDigBio, the Hanes Foundation and the Michigan Consortium of Botanists.

This meeting is focused on bringing small collections in the Great Lakes Region “up to speed”. The workshop is intended to provide curators of small herbaria with the basic knowledge necessary to enable them to begin the digitization process for their collections.  The workshop will include discussions, hands-on demonstrations and guest speakers to address the following questions:

Why is it important to digitize our small/regional collection?
What does it mean to digitize or database our collections?
What are some ways to get our home institutions to support this initiative?
What can we do with digitized data in our research and in the classroom?
How do we get our small/unfunded/unstaffed collections ready for the digitization process?
What are the “need to know” basic mechanics and practical knowledge required to get our specimens online and make them globally available?

Please consider attending and bringing a student. Attendance is limited to 40 attendees. We will provide meals and facilities at no cost to attendees. If you are interested in participating or would like more information, please contact Anna Monfils (monfi1ak@cmich.edu) or Tim Evans (evanstim@gvsu.edu). We would like to have a list of participants by September 21st. Feel free to forward this invitation to other interested parties.
 

Workflow Modules and Task Lists

One outgrowth of the DROID (Developing Robust Object-to-Image-to-Data) workflow workshop held in May 2012 was the establishment of a series of working groups, each focused on workflow modules and tasks for various preparation types. The first of these groups, informally called the Flat Sheets and Packets Working Group, was charged with fleshing out task lists for digitizing vascular and non-vascular plant collections. The second group, Pinned Specimens in Trays and Drawers, is investing its time developing modules to support effective entomological digitization workflows. Other preservation types will follow, concluding with the development of an overall project management module designed to provide guidance for developing and managing digitization projects across disciplines and preservation types.

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